Default Options

There is no option at the moment but I can add a filter in the next update which you could hook into.

This happens also to 404 pages.

In version 1.10.5 you will be able to use something like this to define the defaults.

/**
 * Define post meta defaults
 */
function fp5_post_meta_defaults( $defaults ) {
	$defaults['fp5-no-embed'] = array( 'true' );
	return $defaults;
}
add_filter( 'fp5_post_meta_defaults', 'fp5_post_meta_defaults' );

Is there a documentation of the options?

I have a added list to the plugin GitHub wiki. https://github.com/flowplayer/wordpress-flowplayer/wiki